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Zenodo metadata for the template itself + production API defaults - #38

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annefou merged 2 commits into
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fix/template-zenodo-metadata
Sep 21, 2026
Merged

annefou merged 2 commits into
mainfrom
fix/template-zenodo-metadata

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@annefou

@annefou annefou commented Sep 21, 2026

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The template is now switched on in Zenodo, but its next release would not have archived cleanly. This PR fixes that and updates the skills to use the production API.

1. The template's own Zenodo metadata

CITATION.cff in this repo is a template: {{AUTHOR_FAMILY}}, {{AUTHOR_ORCID}}, date-released: "{{RELEASE_DATE}}"… cffconvert --validate rejects it, so Zenodo cannot build a record from it.

  • Adds .zenodo.json describing the template itself (title, description, Anne Fouilloux + ORCID + LifeWatch ERIC, keywords, MIT). Zenodo's GitHub integration prefers .zenodo.json over CITATION.cff, so the template's release gets clean metadata while CITATION.cff keeps its placeholders for studies.
  • scripts/init_template.py deletes .zenodo.json when a study is initialised, and a dry run reports that it would. Otherwise every replication created from the template would be archived under the template's title and creators. Two new tests cover this; the init-template skill documents it.
  • release-identifiers.yml is unaffected on this repo: its ready-guard already skips while the .template-uninitialised sentinel is present, so it won't write DOIs into the template's placeholder files.

2. Skills default to the production API

  • import-from-nanopub: the sibling-repo curl defaults to https://api.sciencelive4all.org (was api-dev).
  • verify-chain: says the server defaults to production, keeps dev as a commented opt-in so a copy-paste doesn't switch to dev, and adds pipx upgrade forrt-research-mcp, because servers before 0.1.1 still default to dev.

/np/constellation has been on production since 2026-09-20, and forrt-research-mcp 0.1.1 (on PyPI) defaults to it.

Checks

pixi run -e tests pytest: 164 passed (2 new). .zenodo.json is valid JSON.

After merge

Cut v2.1.1 as a GitHub Release. That is the template's first version archived on Zenodo.

The template's CITATION.cff is full of {{placeholders}}, including
date-released and the ORCID, so it is not valid citation metadata (cffconvert
rejects it) and cannot describe the template's own Zenodo record. Add a
.zenodo.json for the template itself; Zenodo's GitHub integration prefers it
over CITATION.cff.

.zenodo.json must not survive into a study created from the template, or every
replication would be archived under the template's title and creators.
init_template.py now deletes it (reported on a dry run too), with two tests.
/np/constellation is on production since 2026-09-20 and forrt-research-mcp
0.1.1 defaults to it. import-from-nanopub's curl now defaults to production
too; verify-chain says so, keeps dev as an explicit opt-in, and tells existing
users to upgrade (pre-0.1.1 servers still default to dev).
@annefou
annefou merged commit 9838ef7 into main Sep 21, 2026
3 checks passed
@annefou
annefou deleted the fix/template-zenodo-metadata branch September 21, 2026 07:12
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